Merged

.gitignore

@@ -6,3 +6,4 @@ __pycache__
 **/venv/**
 **/.idea/**
 .vscode/
+.DS_Store
\ No newline at end of file

build-aws/buildspec.yaml

@@ -26,6 +26,7 @@ env:
     DATA_WORKFLOW_BASE_URL: stub
     FILE_DMS_BASE_URL: stub
     DATASET_REGISTRY_BASE_URL: stub
+    SCHEMA_BASE_URL: stub
     AUTH_TOKEN_URL: stub
     CUSTOM_SCOPE: stub
     ENVIRONMENT: stub
@@ -53,7 +54,7 @@ phases:
       # publish new artifact to code artifact
       - aws codeartifact login --tool twine --domain osdu-dev --domain-owner 888733619319 --repository osdu-python
       - python setup.py sdist bdist_wheel
-      - twine upload --skip-existing --repository codeartifact dist/osdu_api-0.0.4.tar.gz
+      - twine upload --skip-existing --repository codeartifact dist/osdu_api-0.0.5.tar.gz
 
 
 artifacts:

osdu_api/base_client.py

-#  Copyright 2020 Google LLC
-#  Copyright © 2020 Amazon Web Services
+# Copyright © 2020 Amazon Web Services
 #
-#  Licensed under the Apache License, Version 2.0 (the "License");
-#  you may not use this file except in compliance with the License.
-#  You may obtain a copy of the License at
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
 #
 #      http://www.apache.org/licenses/LICENSE-2.0
 #
-#  Unless required by applicable law or agreed to in writing, software
-#  distributed under the License is distributed on an "AS IS" BASIS,
-#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#  See the License for the specific language governing permissions and
-#  limitations under the License.
-
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import sys, os
+import importlib
+from configparser import SafeConfigParser
 import requests
-from osdu_api.libs.configuration.config_manager import ConfigManager
-from osdu_api.libs.context.context import Context
-from osdu_api.libs.exceptions.exceptions import UnknownRequestMethodError, ConfigurationError
-from osdu_api.libs.auth.authorization import TokenRefresher, authorize
 from osdu_api.model.http_method import HttpMethod
 
-
+'''
+Base client that is meant to be extended by service specific clients
+'''
 class BaseClient:
-    """
-    Base client that is meant to be extended by service specific clients.
-    """
 
-    def __init__(self, token_refresher: TokenRefresher, context: Context):
-        self._config_manager = ConfigManager()
-        self.token_refresher = token_refresher
-        self.data_partition_id = context.data_partition_id
+    '''
+    Base client gets initialized with configuration values and a bearer token
+    based on provider-specific logic
+    '''
+    def __init__(self):
+        self._parse_config()
+        self.unauth_retries = 0
+        if self.use_service_principal == 'True' or self.use_service_principal == 'true':
+            self._refresh_service_principal_token()
+    
+    '''
+    Example config file:
+    [environment]
+    data_partition_id=opendes
+    storage_url=https://[STORAGE_ENDPOINT]/api/storage/v2
+    search_url=https://[SEARCH_ENDPOINT]/api/search/v2
+    data_workflow_url=https://[WORKFLOW_ENDPOINT]/api/data-workflow/v1
+    file_dms_url=https://[FILE_DMS_ENDPOINT]/api/filedms/v2
+    dataset_registry_url=https://[DATASET_REGISTRY_URL]/api/dataset-registry/v1
 
-    def get_config_value(self, value: str) -> str:
-        return self._config_manager.get_config_value(value)
+    [provider]
+    name=aws
+    entitlements_module_name=entitlements_client
+    '''
+    def _parse_config(self):
+        config_parser = SafeConfigParser(os.environ)
+        config_file_name = 'osdu_api.ini'
+        found_names = config_parser.read(config_file_name)
+        if config_file_name not in found_names:
+            raise Exception('Could not find osdu_api.ini config file')
 
-    @authorize()
-    def _send_request(self, headers: dict, url: str, params: dict, data: str, method: HttpMethod) -> requests.Response:
-        if method is HttpMethod.GET:
-            response = requests.get(url=url, params=params, headers=headers)
-        elif method is HttpMethod.POST:
-            response = requests.post(url=url, params=params, data=data, headers=headers)
-        elif method is HttpMethod.PUT:
-            response = requests.put(url=url, params=params, data=data, headers=headers)
-        else:
-            raise UnknownRequestMethodError
-        return response
+        self.data_partition_id = config_parser.get('environment', 'data_partition_id')
+        self.storage_url = config_parser.get('environment', 'storage_url')
+        self.search_url = config_parser.get('environment', 'search_url')
+        self.data_workflow_url = config_parser.get('environment', 'data_workflow_url')
+        self.file_dms_url = config_parser.get('environment', 'file_dms_url')
+        self.legal_url = config_parser.get('environment', 'legal_url')
+        self.entitlements_url = config_parser.get('environment', 'entitlements_url')
+        self.dataset_url = config_parser.get('environment', 'dataset_url')
+        self.use_service_principal = config_parser.get('environment', 'use_service_principal')
+
+        self.provider = config_parser.get('provider', 'name')
+        self.service_principal_module_name = config_parser.get('provider', 'service_principal_module_name')
 
-    def make_request(
-            self,
-            method: HttpMethod,
-            url: str,
-            data: str = '',
-            add_headers: dict = None,
-            params: dict = None
-    ) -> requests.Response:
-        """
-        Makes a request using python's built in requests library. Takes additional headers if
-        necessary
-        """
-        params = params or {}
-        add_headers = add_headers or {}
+    
+    '''
+    The path to the logic to get a valid bearer token is dynamically injected based on
+    what provider and entitlements module name is provided in the configuration yaml
+    '''
+    def _refresh_service_principal_token(self):
+        entitlements_client = importlib.import_module('osdu_api.providers.%s.%s' % (self.provider, self.service_principal_module_name))
+        self.service_principal_token = entitlements_client.get_service_principal_token()
+        
+    '''
+    Makes a request using python's built in requests library. Takes additional headers if
+    necessary
+    '''
+    def make_request(self, method: HttpMethod, url: str, data = '', add_headers = {}, params = {}, bearer_token = None):
+        if bearer_token is not None and 'Bearer ' not in bearer_token:
+            bearer_token = 'Bearer ' + bearer_token
+        
         headers = {
             'content-type': 'application/json',
             'data-partition-id': self.data_partition_id,
+            'Authorization': bearer_token if bearer_token is not None else self.service_principal_token
         }
 
-        for key, value in add_headers.items():
-            headers[key] = value
-        response = self._send_request(headers, url, params, data, method)
+        if (len(add_headers) > 0):
+            for key, value in add_headers:
+                headers[key] = value
+
+        response = object
+
+        if (method == HttpMethod.GET):
+            response = requests.get(url=url, params=params, headers=headers, verify=False)
+        elif (method == HttpMethod.DELETE):
+            response = requests.delete(url=url, params=params, headers=headers, verify=False)
+        elif (method == HttpMethod.POST):
+            response = requests.post(url=url, params=params, data=data, headers=headers, verify=False)
+        elif (method == HttpMethod.PUT):
+            response = requests.put(url=url, params=params, data=data, headers=headers, verify=False)
+
+        if (response.status_code == 401 or response.status_code == 403) and self.unauth_retries < 1:
+            if self.use_service_principal == 'True' or self.use_service_principal == 'true':
+                self.unauth_retries += 1
+                self._refresh_service_principal_token()
+                self.make_request(method, url, data, add_headers, params, None)
+        
+        self.unauth_retries = 0
+        
         return response

osdu_api/clients/base_client.py

@@ -63,7 +63,7 @@ class BaseClient:
         self.entitlements_url = config_parser.get('environment', 'entitlements_url')
         self.dataset_url = config_parser.get('environment', 'dataset_url')
         self.use_service_principal = config_parser.get('environment', 'use_service_principal')
-
+        self.schema_url = config_parser.get('environment', 'schema_url')
         self.provider = config_parser.get('provider', 'name')
         self.service_principal_module_name = config_parser.get('provider', 'service_principal_module_name')
 
@@ -90,7 +90,7 @@ class BaseClient:
         }
 
         if (len(add_headers) > 0):
-            for key, value in add_headers:
+            for key, value in add_headers.items():
                 headers[key] = value
 
         response = object
@@ -112,4 +112,4 @@ class BaseClient:
         
         self.unauth_retries = 0
         
-        return response
\ No newline at end of file
+        return response

osdu_api/clients/dataset/dataset_dms_client.py

@@ -23,8 +23,8 @@ class DatasetDmsClient(BaseClient):
     Holds the logic for interfacing with Data Registry Service's DMS api
     """
 
-    def get_storage_instructions(self, resource_type_id: str, bearer_token=None):
-        params = {'resourceType': resource_type_id}
+    def get_storage_instructions(self, kind_sub_type: str, bearer_token=None):
+        params = {'kindSubType': kind_sub_type}
         return self.make_request(method=HttpMethod.GET, url='{}{}'.format(self.dataset_url, '/getStorageInstructions'), 
             params=params, bearer_token=bearer_token)
     

osdu_api/provider/azure/entitlements_client.py → osdu_api/clients/schema/schema_client.py

-# Copyright © Microsoft Corporation
-
+# Copyright © 2020 Amazon Web Services
+#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-# 
+#
 #      http://www.apache.org/licenses/LICENSE-2.0
-# 
+#
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+import json
+from typing import List
+from osdu_api.clients.base_client import BaseClient
+from osdu_api.model.http_method import HttpMethod
+#from osdu_api.model.storage.schema.schema import Schema
+#from osdu_api.model.storage.schema.schema_attribute import SchemaAttribute
 
-import os
-import importlib
-import importlib.util
-from urllib.request import Request, urlopen
-from urllib.parse import urlencode
-from urllib.error import HTTPError
-from json import loads
-
-def get_bearer_token():
-    client_id = os.environ['client_id']
-    client_secret = os.environ['client_secret']
-    tenant_id = os.environ['tenant_id']
-    token_endpoint = os.environ['token_endpoint']
-    resource = os.environ['resource']
+class SchemaClient(BaseClient):
+    """
+    Holds the logic for interfacing with Schema API
+    """
+    def get_schema_by_id(self, schema_id: str, bearer_token=None):
+        return self.make_request(method=HttpMethod.GET, url = '{}/{}/{}'.format(self.schema_url, 'schema', schema_id), 
+                data={}, bearer_token=bearer_token)
 
-    body = {
-            "grant_type": "client_credentials",
-            "client_id": client_id,
-            "client_secret": client_secret,
-            "resource":resource
-        }
-        
-    headers = {
-            "Content-Type": "application/x-www-form-urlencoded"
-        }
-    data = urlencode(body).encode("utf8")
-    request = Request(url=token_endpoint, data=data, headers=headers)
-    try:
-        response = urlopen(request)
-        response_body = response.read()
-        resp = loads(response_body)
-        token = resp["access_token"]
-    except HTTPError:
-        raise
-    return f'Bearer {token}'

osdu_api/examples/osdu_api.ini

-# Copyright © 2020 Amazon Web Services
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#      http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-[environment]
-data_partition_id=opendes
-storage_url=%(BASE_URL)s/api/storage/v2
-search_url=%(BASE_URL)s/api/search/v2
-legal_url=%(BASE_URL)s/api/legal/v1
-data_workflow_url=%(BASE_URL)s/api/data-workflow/v1
-file_dms_url=%(BASE_URL)s/api/filedms/v2
-dataset_url=%(BASE_URL)s/api/dataset-registry/v1
-entitlements_url=%(BASE_URL)s/api/entitlements/v1
-use_service_principal=False
-
-[provider]
-name=aws
-service_principal_module_name=service_principal_util
-token_url_ssm_path=/osdu/%(ENVIRONMENT)s/oauth-token-uri
-aws_oauth_custom_scope_ssm_path=/osdu/%(ENVIRONMENT)s/oauth-custom-scope
-client_id_ssm_path=/osdu/%(ENVIRONMENT)s/client-credentials-client-id
-client_secret_name=/osdu/%(ENVIRONMENT)s/client_credentials_secret
-client_secret_dict_key=client_credentials_client_secret
-region_name=%(AWS_REGION)s
+ # Copyright © 2020 Amazon Web Services
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #      http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+ [environment]
+ data_partition_id=opendes
+ storage_url=%(BASE_URL)s/api/storage/v2
+ search_url=%(BASE_URL)s/api/search/v2
+ legal_url=%(BASE_URL)s/api/legal/v1
+ data_workflow_url=%(BASE_URL)s/api/data-workflow/v1
+ file_dms_url=%(BASE_URL)s/api/filedms/v2
+ dataset_url=%(BASE_URL)s/api/dataset-registry/v1
+ entitlements_url=%(BASE_URL)s/api/entitlements/v1
+ schema_url=%(BASE_URL)s/api/schema-service/v1
+ use_service_principal=True
+ 
+ [provider]
+ name=aws
+ service_principal_module_name=service_principal_util
+ token_url_ssm_path=/osdu/%(ENVIRONMENT)s/oauth-token-uri
+ aws_oauth_custom_scope_ssm_path=/osdu/%(ENVIRONMENT)s/oauth-custom-scope
+ client_id_ssm_path=/osdu/%(ENVIRONMENT)s/client-credentials-client-id
+ client_secret_name=/osdu/%(ENVIRONMENT)s/client_credentials_secret
+ client_secret_dict_key=client_credentials_client_secret
+ region_name=%(AWS_REGION)s

osdu_api/libs/auth/authorization.py

@@ -20,7 +20,7 @@ from functools import partial
 from http import HTTPStatus
 
 import requests
-from osdu_api.libs.exceptions.exceptions import TokenRefresherNotPresentError
+from osdu_api.libs.exceptions import TokenRefresherNotPresentError
 
 logger = logging.getLogger()
 

osdu_api/libs/configuration/config_manager.py

@@ -17,7 +17,7 @@ import enum
 import os
 
 import yaml
-from osdu_api.libs.exceptions.exceptions import ConfigurationError
+from osdu_api.libs.exceptions import ConfigurationError
 
 """
 This module is used for initializing configurations, such as OSDU API endpoints, vendor info etc.

osdu_api/search/search_client.py → osdu_api/libs/constants.py

 #  Copyright 2020 Google LLC
-#  Copyright © 2020 Amazon Web Services
+#  Copyright 2020 EPAM Systems
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
 #  you may not use this file except in compliance with the License.
@@ -13,26 +13,27 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 
-import json
-from typing import List
-from osdu_api.base_client import BaseClient
-from osdu_api.model.http_method import HttpMethod
-from osdu_api.model.search.query_response import QueryResponse
+"""Constants module."""
 
-'''
-Holds the logic for interfacing with Search's query api
-'''
-class SearchClient(BaseClient):
+RETRIES = 3
+TIMEOUT = 1
+WAIT = 10
 
-    '''
-    Used to hit search's api endpoint "queryRecords"
-    '''
-    def query_records_from_dict(self, query_request: dict):
-        query_request_data = json.dumps(query_request)
+FIRST_STORED_RECORD_INDEX = 0
 
-        response = self.make_request(method=HttpMethod.POST, url=self.search_url, data=query_request_data)
-        response_content = json.loads(response.content)
-        query_response = QueryResponse(response_content['results'], response_content['aggregations'])
-
-        return query_response
+# Paths to extend schema fields with surrogate keys
+DATA_TYPES_WITH_SURROGATE_KEYS = ("dataset", "work-product", "work-product-component")
+SURROGATE_KEYS_PATHS = [
+    ("definitions", "{{data-partition-id}}:wks:AbstractWPCGroupType:1.0.0", "properties", "Datasets",
+     "items"),
+    ("definitions", "osdu:wks:AbstractWPCGroupType:1.0.0", "properties", "Artefacts",
+     "items", "properties", "ResourceID"),
+    ("properties", "data", "allOf", 1, "properties", "Components", "items"),
+]
 
+DATA_SECTION = "Data"
+DATASETS_SECTION = "Datasets"
+MASTER_DATA_SECTION ="MasterData"
+REFERENCE_DATA_SECTION ="ReferenceData"
+WORK_PRODUCT_SECTION = "WorkProduct"
+WORK_PRODUCT_COMPONENTS_SECTION = "WorkProductComponents"

osdu_api/libs/context/context.py → osdu_api/libs/context.py

@@ -13,23 +13,27 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 
+"""Context module."""
 
 import dataclasses
 
 
 @dataclasses.dataclass
-class Context(object):
-    """
-    Store data-partition-id and AppKey passed via Payload field of dagrun.conf.
-    """
+class Context:
+    """Class to store data-partition-id and AppKey."""
+
     data_partition_id: str
     app_key: str
 
     @classmethod
     def populate(cls, ctx: dict) -> 'Context':
+        """
+        Populates Context dataclass from dagrun.conf dict.
+
+        :return: populated Context
+        :rtype: Context
+        """
         ctx_payload = ctx.pop('Payload')
-        ctx_obj = cls(
-            app_key=ctx_payload['AppKey'],
-            data_partition_id=ctx_payload['data-partition-id']
-        )
+        ctx_obj = cls(app_key=ctx_payload['AppKey'],
+                      data_partition_id=ctx_payload['data-partition-id'])
         return ctx_obj

osdu_api/libs/exceptions.py

+#  Copyright 2020 Google LLC
+#  Copyright 2020 EPAM Systems
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+"""Exceptions module."""
+
+
+class RecordsNotSearchableError(Exception):
+    """Raise when expected totalCount of records differs from actual one."""
+    pass
+
+
+class PipelineFailedError(Exception):
+    """Raise when pipeline failed."""
+    pass
+
+
+class EmptyManifestError(Exception):
+    """Raise when manifest field is empty."""
+    pass
+
+
+class GetSchemaError(Exception):
+    """Raise when can't find schema."""
+    pass
+
+
+class SRNNotFound(Exception):
+    """Raise when can't find SRN."""
+    pass
+
+
+class NotOSDUSchemaFormatError(Exception):
+    """Raise when schema doesn't correspond OSDU format."""
+    pass
+
+
+class FileSourceError(Exception):
+    """Raise when file doesn't exist under given URI path."""
+    pass
+
+
+class UploadFileError(Exception):
+    """Raise when there is an error while uploading a file into OSDU."""
+
+
+class TokenRefresherNotPresentError(Exception):
+    """Raise when token refresher is not present in "refresh_token' decorator."""
+    pass
+
+
+class NoParentEntitySystemSRNError(Exception):
+    """Raise when parent entity doesn't have system-generated SRN."""
+    pass
+
+
+class NoParentEntitySystemSRNError(Exception):
+    """
+    Raise when parent entity doesn't have system-generated SRN.
+    """
+    pass
+
+
+class InvalidFileRecordData(Exception):
+    """Raise when file data does not contain mandatory fields."""
+
+
+class GenericManifestSchemaError(Exception):
+    """Raise when a generic manifest schema is invalid."""

osdu_api/libs/handle_file.py

+#  Copyright 2020 Google LLC
+#  Copyright 2020 EPAM Systems
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+"""This module provides cloud specific File Handler implementations."""
+
+import dataclasses
+import io
+import json
+import logging
+import uuid
+from typing import List, Tuple, TypeVar
+
+import requests
+import tenacity
+from osdu_api.libs.constants import RETRIES, WAIT
+from osdu_api.libs.context import Context
+from osdu_api.libs.exceptions import InvalidFileRecordData
+from osdu_api.libs.mixins import HeadersMixin
+from osdu_api.libs.auth.authorization import TokenRefresher, authorize
+from osdu_api.providers import blob_storage
+from osdu_api.providers.types import BlobStorageClient, FileLikeObject
+
+logger = logging.getLogger()
+
+RETRY_SETTINGS = {
+    "stop": tenacity.stop_after_attempt(RETRIES),
+    "wait": tenacity.wait_fixed(WAIT),
+}
+
+
+@dataclasses.dataclass
+class FileUploadUrlResponse:
+    """Simple class to store File service uploadURL response values."""
+    file_id: str
+    signed_url: str
+    file_source: str
+